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Processing natural language with biomolecules: where linguistics, biology and computation meet. (English) Zbl 07627924

Berger, Ulrich (ed.) et al., Revolutions and revelations in computability. 18th conference on computability in Europe, CiE 2022, Swansea, UK, July 11–15, 2022. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 13359, 139-150 (2022).

MSC: 68Qxx

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Chowdhury, Rochishnu; Egan, Raphael; Bochkov, Daniil; Gibou, Frederic

Efficient calculation of fully resolved electrostatics around large biomolecules. (English) Zbl 1537.65156

J. Comput. Phys. 448, Article ID 110718, 17 p. (2022).

MSC: 65N08 65Y05 78A30

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Xu, Xining; Zhang, Yunxin

Motility and energetics of randomly flashing ratchets. (English) Zbl 1504.82038

J. Stat. Mech. Theory Exp. 2021, No. 3, Article ID 033503, 21 p. (2021).

MSC: 82C31 60J70 92C45

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Masood, Talha Bin; Ray, Tathagata; Natarajan, Vijay

Parallel computation of alpha complexes for biomolecules. (English) Zbl 07760146

Cabello, Sergio (ed.) et al., 36th international symposium on computational geometry, SoCG 2020, Zürich, Switzerland (virtual conference), June 23–26, 2020. Proceedings. Wadern: Schloss Dagstuhl – Leibniz Zentrum für Informatik. LIPIcs – Leibniz Int. Proc. Inform. 164, Article 17, 16 p. (2020).

MSC: 68-XX

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Ionescu, Daniela; Apreotesei, Gabriela

Detection of the biological constituents in solution using metamaterial slabs with special properties. (English) Zbl 1488.92027

Bul. Inst. Politeh. Iași, Secț. I, Mat. Mec. Teor. Fiz. 66(70), No. 4, 9-18 (2020).

MSC: 92C40

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Sharma, Shivangi; Biswas, Parbati

Conformational transitions of a DNA hairpin through transition path times. (English) Zbl 1459.92068

J. Stat. Mech. Theory Exp. 2020, No. 7, Article ID 073411, 29 p. (2020).

MSC: 92D20 60J70

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Masood, Talha Bin; Ray, Tathagata; Natarajan, Vijay

Parallel computation of alpha complexes for biomolecules. (English) Zbl 1453.92105

Comput. Geom. 90, Article ID 101651, 16 p. (2020).

MSC: 92C40 68W10

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Knobloch, Christian; Stickler, Benjamin A.; Brand, Christian; Sclafani, Michele; Lilach, Yigal; Juffmann, Thomas; Cheshnovsky, Ori; Hornberger, Klaus; Arndt, Markus

On the role of the electric dipole moment in the diffraction of biomolecules at nanomechanical gratings. (English) Zbl 1371.92053

Fortschr. Phys. 65, No. 6-8, 1600025, 8 p. (2017).

MSC: 92C40 78M16 92E10 82D80 81U10

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Gutman, Ivan

Frank model with limited resources. (English) Zbl 1307.80006

J. Math. Chem. 52, No. 9, 2330-2333 (2014).

MSC: 80A30 92E20

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Liwo, Adam (ed.)

Computational methods to study the structure and dynamics of biomolecules and biomolecular processes. From bioinformatics to molecular quantum mechanics. (English) Zbl 1298.92011

Springer Series in Bio-/Neuroinformatics 1. Berlin: Springer (ISBN 978-3-642-28553-0/hbk; 978-3-642-28554-7/ebook). xiii, 810 p. (2014).

MSC: 92-06 92-08 92C40 92C45 92D20 00B15

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Fackeldey, Konstantin; Klimm, Martina; Weber, Marcus

A coarse graining method for the dimension reduction of the state space of biomolecules. (English) Zbl 1309.92036

J. Math. Chem. 50, No. 9, 2623-2635 (2012).

MSC: 92C40

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Fadeev, S. I.; Likhoshvaj, V. A.; Shtokalo, D. N.

Letter to the editor. (Russian) Zbl 1233.92016

Sib. Zh. Ind. Mat. 14, No. 1, 150 (2011).

Reviewer: Victor Alexandrov (Novosibirsk)

MSC: 92C40 92D20

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Geng, Weihua; Wei, G. W.

Multiscale molecular dynamics using the matched interface and boundary method. (English) Zbl 1246.82028

J. Comput. Phys. 230, No. 2, 435-457 (2011).

MSC: 82B24 78A70 82-08 92C40

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Weggler, S.; Rutka, V.; Hildebrandt, A.

A new numerical method for nonlocal electrostatics in biomolecular simulations. (English) Zbl 1193.92006

J. Comput. Phys. 229, No. 11, 4059-4074 (2010).

MSC: 92C05 78A70 78M20

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Iorio, Alfredo; Sen, Samik; Sen, Siddhartha

Do quantum effects hold together DNA condensates? (English) Zbl 1186.82115

Int. J. Mod. Phys. B 24, No. 3, 323-330 (2010).

MSC: 82D60 92D20 78A57 78A35

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Souaille, M.; Loirat, H.; Borgis, D.; Gaigeot, M. P.

MDVRY: a polarizable classical molecular dynamics package for biomolecules. (English) Zbl 1198.82058

Comput. Phys. Commun. 180, No. 2, 276-301 (2009).

MSC: 82C80 92E10

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Cuco, Ana Paula C.; Silva Neto, Antônio J.; Campos Velho, Haroldo F.; de Sousa, Fabiano L.

Solution of an inverse adsorption problem with an epidemic genetic algorithm and the generalized extremal optimization algorithm. (English) Zbl 1165.65028

Inverse Probl. Sci. Eng. 17, No. 3, 289-302 (2009).

MSC: 65K05 90C15 92C45 92-08

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Du Toit, Philip; Mezić, Igor; Marsden, Jerrold

Coupled oscillator models with no scale separation. (English) Zbl 1157.37343

Physica D 238, No. 5, 490-501 (2009).

MSC: 37N25 34C15 34C20

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Cai, Wei; Xu, Zhenli; Baumketner, Andrij

A new FFT-based algorithm to compute Born radii in the generalized Born theory of biomolecule solvation. (English) Zbl 1154.82322

J. Comput. Phys. 227, No. 24, 10162-10177 (2008).

MSC: 82C80 81V55 65T50 92C99

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Liu, Yaling; Liu, Wing Kam; Belytschko, Ted; Patankar, Neelesh; To, Albert C.; Kopacz, Adrian; Chung, Jae-Hyun

Immersed electrokinetic finite element method. (English) Zbl 1194.76126

Int. J. Numer. Methods Eng. 71, No. 4, 379-405 (2007).

MSC: 76M10 76W05 76T20

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Schmiedl, Tim; Speck, Thomas; Seifert, Udo

Entropy production for mechanically or chemically driven biomolecules. (English) Zbl 1117.82032

J. Stat. Phys. 128, No. 1-2, 77-93 (2007).

MSC: 82C31 92C40 92C45 82C35

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Chouaieb, Nadia; Goriely, Alain; Maddocks, John H.

Helices. (English) Zbl 1160.74373

Proc. Natl. Acad. Sci. USA 103, No. 25, 9398-9403 (2006).

MSC: 74K10 53A04 74L15 92C40

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Jarzynski, Christopher

Work fluctuation theorems and single-molecule biophysics. (English) Zbl 1115.82349

Ohta, Takao (ed.) et al., Physics of non-equilibrium systems: selforganized structures and dynamics far from equilibrium. Proceedings of the 20th Nishinomiya-Yukawa memorial symposium, October 3 and 4, Nishinomiya, Japan. Kyoto: Progress of Theoretical Physics. Progress of Theoretical Physics. Supplement 165, 1-17 (2006).

MSC: 82D60 92C05

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Patel, Sandeep; Brooks, Charles L.

Fluctuating charge force fields: recent developments and applications from small molecules to macromolecular biological systems. (English) Zbl 1173.81357

Mol. Simul. 32, No. 3-4, 231-249 (2006).

MSC: 81V55

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Ritter, Silke; Odenheimer, Jens; Heermann, Dieter W.; Bantignies, Frederic; Grimaud, Charlotte; Cavalli, Giacomo

Modelling of polycomb-dependent chromosomal interactions involved in drosophila gene silencing. (English) Zbl 1107.82433

Int. J. Mod. Phys. C 17, No. 5, 757-767 (2006).

MSC: 82D60 92C40 92D10

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Makrodimitris, Kosta; Fernandez, Erik J.; Woolf, Thomas B.; O’Connell, John P.

ALLD: an object-oriented mesoscopic simulation program for polar biomolecules in hydrophobic chromatography or biomembranes. (English) Zbl 1096.92018

Mol. Simul. 31, No. 9, 623-636 (2005).

MSC: 92C40 65C20

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Meerbach, Eike; Schütte, Christof; Fischer, Alexander

Eigenvalue bounds on restrictions of reversible nearly uncoupled Markov chains. (English) Zbl 1076.15018

Linear Algebra Appl. 398, 141-160 (2005).

Reviewer: Huang Wenxue (Scarborough)

MSC: 15A42 15B51 60J10

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Schütte, Christof; Forster, Ralf; Meerbach, Eike; Fischer, Alexander

Uncoupling-coupling techniques for metastable dynamical systems. (English) Zbl 1066.65010

Kornhuber, Ralf (ed.) et al., Domain decomposition methods in science and engineering. Selected papers of the 15th international conference on domain decomposition, Berlin, Germany, July 21–25, 2003. Berlin: Springer (ISBN 3-540-22523-4/pbk). Lecture Notes in Computational Science and Engineering 40, 115-129 (2005).

MSC: 65C05 65C40 65C30 60H35 60J22 92C40

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Sariyanni, Zoe-Elizabeth; Rostovtsev, Yuri

Generation and propagation of a resonant CARS signal from biomolecules: application to dispicolinic acid. (English) Zbl 1060.78533

J. Mod. Opt. 51, No. 16-18, 2637-2644 (2004).

MSC: 78A60

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Stocker, Urs; Juchli, Daniel; van Gunsteren, Wilfred F.

Increasing the time step and efficiency of molecular dynamics simulations: Optimal solutions for equilibrium simulations or structure refinement of large biomolecules. (English) Zbl 1015.92007

Mol. Simul. 29, No. 2, 123-138 (2003).

MSC: 92C05 65C20 92C40

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Ebeling, Werner; Schimansky-Geier, Lutz; Romanovsky, Yuri M.

Stochastic dynamics reacting biomolecules. (English) Zbl 1050.92024

River Edge, NJ: World Scientific (ISBN 981-238-162-7/hbk). xxiii, 318 p. (2002).

Reviewer: H. R. Hirsch (Lexington)

MSC: 92C45 92C05 92-02 92C40 37N25 37H99 80A32

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Garzon, Max H. (ed.); Conrad, Michael (ed.)

Special issue on soft computing in biomolecules. (English) Zbl 1013.00505

Soft Comput. 5, No. 1, 92 p. (2001).

MSC: 00B15 68-06 68Q05 68Q10

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Schütte, Ch.; Huisinga, W.

On conformational dynamics induced by Langevin processes. (English) Zbl 0978.92010

Fiedler, B. (ed.) et al., International conference on differential equations. Proceedings of the conference, Equadiff ’99, Berlin, Germany, August 1-7, 1999. Vol. 2. Singapore: World Scientific. 1247-1262 (2000).

MSC: 92C40 37N25 82C31

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Kurzyński, Michał

Internal dynamics of biomolecules and statistical theory of biochemical processes. (English) Zbl 1059.92501

Physica A 285, No. 1-2, 29-47 (2000).

MSC: 92C40 82D99 60G35

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Pančoška, Petr; Janota, Vít; Nešetřil, Jaroslav

Spectra, graphs and proteins. Towards understanding of protein folding. (English) Zbl 0931.05081

Graham, Ronald L. (ed.) et al., Contemporary trends in discrete mathematics. From DIMACS and DIMATIA to the future. Proceedings of the DIMATIA-DIMACS conference, Štiřín Castle, Czech Republic, May 19–25, 1997. Providence, RI: American Mathematical Society. DIMACS, Ser. Discrete Math. Theor. Comput. Sci. 49, 237-255 (1999).

MSC: 05C90 92D20

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Chikishev, Andrej Yu.; Netrebko, Nina V.; Romanovsky, Youri M.; Ebeling, Werner; Schimansky-Geier, Lutz; Netrebko, Aleksej V.

Stochastic cluster dynamics of macromolecules. (English) Zbl 0936.82016

Int. J. Bifurcation Chaos Appl. Sci. Eng. 8, No. 4-5, 921-926 (1998).

MSC: 82C31 92C40

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Moroz, J. David; Kamien, Randall D.

Self-avoiding walks with writhe. (English) Zbl 0925.82103

Nucl. Phys., B 506, No. 3, 695-710 (1997).

MSC: 82B41 81T13 82B27

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Yagil, G.

On the structural complexity of designed systems. (English) Zbl 0852.92001

Nadel, Lynn (ed.) et al., 1992 lectures in complex systems. Papers from the summer school held in Santa Fe, NM, USA, 1992. Reading, MA: Addison-Wesley. St. Fe Inst. Stud. Sci. Complexity, Lect. 5, 519-530 (1993).

MSC: 92B05 92E10

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Schreiber, H.; Steinhauser, O.; Schuster, P.

Parallel molecular dynamics of biomolecules. (English) Zbl 0752.92013

Parallel Comput. 18, No. 5, 557-573 (1992).

MSC: 92C40 92-08 65Y05

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Thompson, Colin J.

Mathematical statistical mechanics. (English) Zbl 0417.60096

Princeton, New Jersey: Princeton University Press. X. 278 p. $ 7.50 (1979).

MSC: 60K35 82-01 82B05 82B26

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Nussinov, Ruth; Pieczenik, George; Griggs, Jerrold R.; Kleitman, Daniel J.

Algorithms for loop matchings. (English) Zbl 0411.92008

SIAM J. Appl. Math. 35, 68-82 (1978).

MSC: 92Cxx 90C39 92D10

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Found 41 Documents (Results 1–41)

Processing natural language with biomolecules: where linguistics, biology and computation meet. (English) Zbl 07627924

Efficient calculation of fully resolved electrostatics around large biomolecules. (English) Zbl 1537.65156

Motility and energetics of randomly flashing ratchets. (English) Zbl 1504.82038

Parallel computation of alpha complexes for biomolecules. (English) Zbl 07760146

Detection of the biological constituents in solution using metamaterial slabs with special properties. (English) Zbl 1488.92027

Conformational transitions of a DNA hairpin through transition path times. (English) Zbl 1459.92068

Parallel computation of alpha complexes for biomolecules. (English) Zbl 1453.92105

On the role of the electric dipole moment in the diffraction of biomolecules at nanomechanical gratings. (English) Zbl 1371.92053

Frank model with limited resources. (English) Zbl 1307.80006

Computational methods to study the structure and dynamics of biomolecules and biomolecular processes. From bioinformatics to molecular quantum mechanics. (English) Zbl 1298.92011

A coarse graining method for the dimension reduction of the state space of biomolecules. (English) Zbl 1309.92036

Letter to the editor. (Russian) Zbl 1233.92016

Multiscale molecular dynamics using the matched interface and boundary method. (English) Zbl 1246.82028

A new numerical method for nonlocal electrostatics in biomolecular simulations. (English) Zbl 1193.92006

Do quantum effects hold together DNA condensates? (English) Zbl 1186.82115

MDVRY: a polarizable classical molecular dynamics package for biomolecules. (English) Zbl 1198.82058

Solution of an inverse adsorption problem with an epidemic genetic algorithm and the generalized extremal optimization algorithm. (English) Zbl 1165.65028

Coupled oscillator models with no scale separation. (English) Zbl 1157.37343

A new FFT-based algorithm to compute Born radii in the generalized Born theory of biomolecule solvation. (English) Zbl 1154.82322

Immersed electrokinetic finite element method. (English) Zbl 1194.76126

Entropy production for mechanically or chemically driven biomolecules. (English) Zbl 1117.82032

Helices. (English) Zbl 1160.74373

Work fluctuation theorems and single-molecule biophysics. (English) Zbl 1115.82349

Fluctuating charge force fields: recent developments and applications from small molecules to macromolecular biological systems. (English) Zbl 1173.81357

Modelling of polycomb-dependent chromosomal interactions involved in drosophila gene silencing. (English) Zbl 1107.82433

ALLD: an object-oriented mesoscopic simulation program for polar biomolecules in hydrophobic chromatography or biomembranes. (English) Zbl 1096.92018

Eigenvalue bounds on restrictions of reversible nearly uncoupled Markov chains. (English) Zbl 1076.15018

Uncoupling-coupling techniques for metastable dynamical systems. (English) Zbl 1066.65010

Generation and propagation of a resonant CARS signal from biomolecules: application to dispicolinic acid. (English) Zbl 1060.78533

Increasing the time step and efficiency of molecular dynamics simulations: Optimal solutions for equilibrium simulations or structure refinement of large biomolecules. (English) Zbl 1015.92007

Stochastic dynamics reacting biomolecules. (English) Zbl 1050.92024

Special issue on soft computing in biomolecules. (English) Zbl 1013.00505

On conformational dynamics induced by Langevin processes. (English) Zbl 0978.92010

Internal dynamics of biomolecules and statistical theory of biochemical processes. (English) Zbl 1059.92501

Spectra, graphs and proteins. Towards understanding of protein folding. (English) Zbl 0931.05081

Stochastic cluster dynamics of macromolecules. (English) Zbl 0936.82016

Self-avoiding walks with writhe. (English) Zbl 0925.82103

On the structural complexity of designed systems. (English) Zbl 0852.92001

Parallel molecular dynamics of biomolecules. (English) Zbl 0752.92013

Mathematical statistical mechanics. (English) Zbl 0417.60096

Algorithms for loop matchings. (English) Zbl 0411.92008

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